| | Editorial Nucleic Acids Res. 2007 July; 35(Web Server issue): W1. Published online 2007 July. doi: 10.1093/nar/gkm484.PMCID: PMC1933172 Articles Conducting Research on the Web: 2007 Update for the Bioinformatics Links Directory Joanne A. Fox, Scott McMillan, and B. F. Francis Ouellette PMCID: PMC1933129 Web Services at the European Bioinformatics Institute Alberto Labarga, Franck Valentin, Mikael Anderson, and Rodrigo Lopez PMCID: PMC1933145 eTBLAST: a web server to identify expert reviewers, appropriate journals and similar publications Mounir Errami, Jonathan D. Wren, Justin M. Hicks, and Harold R. Garner PMCID: PMC1933238 CARGO: a web portal to integrate customized biological information Ildefonso Cases, David G. Pisano, Eduardo Andres, Angel Carro, José M. Fernández, Gonzalo Gómez-López, Jose M. Rodriguez, Jaime F. Vera, Alfonso Valencia, and Ana M. Rojas PMCID: PMC1933121 iHOP web services José M. Fernández, Robert Hoffmann, and Alfonso Valencia PMCID: PMC1933131 Berkeley Phylogenomics Group web servers: resources for structural phylogenomic analysis Jake Gunn Glanville, Dan Kirshner, Nandini Krishnamurthy, and Kimmen Sjölander PMCID: PMC1933202 MultiPhyl: a high-throughput phylogenomics webserver using distributed computing Thomas M. Keane, Thomas J. Naughton, and James O. McInerney PMCID: PMC1933173 Phylemon: a suite of web tools for molecular evolution, phylogenetics and phylogenomics Joaquín Tárraga, Ignacio Medina, Leonardo Arbiza, Jaime Huerta-Cepas, Toni Gabaldón, Joaquín Dopazo, and Hernán Dopazo PMCID: PMC1933211 OligoCalc: an online oligonucleotide properties calculator Warren A. Kibbe PMCID: PMC1933198 RF-DYMHC: detecting the yeast meiotic recombination hotspots and coldspots by random forest model using gapped dinucleotide composition features Peng Jiang, Haonan Wu, Jiawei Wei, Fei Sang, Xiao Sun, and Zuhong Lu PMCID: PMC1933199 CRISPRFinder: a web tool to identify clustered regularly interspaced short palindromic repeats Ibtissem Grissa, Gilles Vergnaud, and Christine Pourcel PMCID: PMC1933234 REPK: an analytical web server to select restriction endonucleases for terminal restriction fragment length polymorphism analysis Roy Eric Collins and Gabrielle Rocap PMCID: PMC1933217 PrimerZ: streamlined primer design for promoters, exons and human SNPs Ming-Fang Tsai, Yi-Jung Lin, Yu-Chang Cheng, Kuo-Hsi Lee, Cheng-Chih Huang, Yuan-Tsong Chen, and Adam Yao PMCID: PMC1933185 NTMG (N-terminal Truncated Mutants Generator for cDNA): an automatic multiplex PCR assays design for generating various N-terminal truncated cDNA mutants Yung-Fu Chen, Rung-Ching Chen, Lin-Yu Tseng, Elong Lin, Yung-Kuan Chan, and Ren-Hao Pan PMCID: PMC1933230 Primer3Plus, an enhanced web interface to Primer3 Andreas Untergasser, Harm Nijveen, Xiangyu Rao, Ton Bisseling, René Geurts, and Jack A.M. Leunissen PMCID: PMC1933133 Asterias: integrated analysis of expression and aCGH data using an open-source, web-based, parallelized software suite Ramón Díaz-Uriarte, Andreu Alibés, Edward R. Morrissey, Andrés Cañada, Oscar M. Rueda, and Mariana L. Neves PMCID: PMC1933128 ISACGH: a web-based environment for the analysis of Array CGH and gene expression which includes functional profiling Lucía Conde, David Montaner, Jordi Burguet-Castell, Joaquín Tárraga, Ignacio Medina, Fátima Al-Shahrour, and Joaquín Dopazo PMCID: PMC1933149 MAGMA: analysis of two-channel microarrays made easy Hubert Rehrauer, Stefan Zoller, and Ralph Schlapbach PMCID: PMC1933123 FatiGO +: a functional profiling tool for genomic data. Integration of functional annotation, regulatory motifs and interaction data with microarray experiments Fátima Al-Shahrour, Pablo Minguez, Joaquín Tárraga, Ignacio Medina, Eva Alloza, David Montaner, and Joaquín Dopazo PMCID: PMC1933151 MobilomeFINDER: web-based tools for in silico and experimental discovery of bacterial genomic islands Hong-Yu Ou, Xinyi He, Ewan M. Harrison, Bridget R. Kulasekara, Ali Bin Thani, Aras Kadioglu, Stephen Lory, Jay C. D. Hinton, Michael R. Barer, Zixin Deng, and Kumar Rajakumar PMCID: PMC1933208 Cross-species microarray analysis with the OSCAR system suggests an INSR->Pax6->NQO1 neuro-protective pathway in aging and Alzheimer's disease Yue Lu, Xin He, and Sheng Zhong PMCID: PMC1933158 QuickSNP: an automated web server for selection of tagSNPs Deepak Grover, Alonzo S. Woodfield, Ranjana Verma, Peter P. Zandi, Douglas F. Levinson, and James B. Potash PMCID: PMC1933212 FGF: A web tool for Fishing Gene Family in a whole genome database Hongkun Zheng, Junjie Shi, Xiaodong Fang, Yuan Li, Søren Vang, Wei Fan, Junyi Wang, Zhang Zhang, Wen Wang, Karsten Kristiansen, and Jun Wang PMCID: PMC1933194 OPTIMIZER: a web server for optimizing the codon usage of DNA sequences Pere Puigbò, Eduard Guzmán, Antoni Romeu, and Santiago Garcia-Vallvé PMCID: PMC1933141 CodonO: codon usage bias analysis within and across genomes Michael C. Angellotti, Shafquat B. Bhuiyan, Guorong Chen, and Xiu-Feng Wan PMCID: PMC1933134 WebTraceMiner: a web service for processing and mining EST sequence trace files Chun Liang, Gang Wang, Lin Liu, Guoli Ji, Yuansheng Liu, Jinqiao Chen, Jason S. Webb, Greg Reese, and Jeffrey F. D. Dean PMCID: PMC1933163 ESTExplorer: an expressed sequence tag (EST) assembly and annotation platform Shivashankar H. Nagaraj, Nandan Deshpande, Robin B. Gasser, and Shoba Ranganathan PMCID: PMC1933243 Wheat Estimated Transcript Server (WhETS): a tool to provide best estimate of hexaploid wheat transcript sequence Rowan A. C. Mitchell, Nathalie Castells-Brooke, Jan Taubert, Paul J. Verrier, David J. Leader, and Christopher J. Rawlings PMCID: PMC1933201 GeneHub-GEPIS: digital expression profiling for normal and cancer tissues based on an integrated gene database Yan Zhang, Shiuh-Ming Luoh, Lawrence S. Hon, Robert Baertsch, William I. Wood, and Zemin Zhang PMCID: PMC1933245 ESTpass: a web-based server for processing and annotating expressed sequence tag (EST) sequences Byungwook Lee, Taehui Hong, Sang Jin Byun, Taeha Woo, and Yoon Jeong Choi PMCID: PMC1933161 SAGExplore: a web server for unambiguous tag mapping in serial analysis of gene expression oriented to gene discovery and annotation Tomás Norambuena, Rodrigo Malig, and Francisco Melo PMCID: PMC1933165 DAVID Bioinformatics Resources: expanded annotation database and novel algorithms to better extract biology from large gene lists Da Wei Huang, Brad T. Sherman, Qina Tan, Joseph Kir, David Liu, David Bryant, Yongjian Guo, Robert Stephens, Michael W. Baseler, H. Clifford Lane, and Richard A. Lempicki PMCID: PMC1933169 PathExpress: a web-based tool to identify relevant pathways in gene expression data Nicolas Goffard and Georg Weiller PMCID: PMC1933187 KAAS: an automatic genome annotation and pathway reconstruction server Yuki Moriya, Masumi Itoh, Shujiro Okuda, Akiyasu C. Yoshizawa, and Minoru Kanehisa PMCID: PMC1933193 GeneTrail—advanced gene set enrichment analysis Christina Backes, Andreas Keller, Jan Kuentzer, Benny Kneissl, Nicole Comtesse, Yasser A. Elnakady, Rolf Müller, Eckart Meese, and Hans-Peter Lenhof PMCID: PMC1933132 g:Profiler—a web-based toolset for functional profiling of gene lists from large-scale experiments Jüri Reimand, Meelis Kull, Hedi Peterson, Jaanus Hansen, and Jaak Vilo PMCID: PMC1933153 MADAP, a flexible clustering tool for the interpretation of one-dimensional genome annotation data Christoph D. Schmid, Thierry Sengstag, Philipp Bucher, and Mauro Delorenzi PMCID: PMC1933235 Onto-Tools: new additions and improvements in 2006 Purvesh Khatri, Calin Voichita, Khalid Kattan, Nadeem Ansari, Avani Khatri, Constantin Georgescu, Adi L. Tarca, and Sorin Draghici PMCID: PMC1933142 Update of the G2D tool for prioritization of gene candidates to inherited diseases Carolina Perez-Iratxeta, Peer Bork, and Miguel A. Andrade-Navarro PMCID: PMC1933178 WebMOTIFS: automated discovery, filtering and scoring of DNA sequence motifs using multiple programs and Bayesian approaches Katherine A. Romer, Guy-Richard Kayombya, and Ernest Fraenkel PMCID: PMC1933171 MYBS: a comprehensive web server for mining transcription factor binding sites in yeast Huai-Kuang Tsai, Meng-Yuan Chou, Ching-Hua Shih, Grace Tzu-Wei Huang, Tien-Hsien Chang, and Wen-Hsiung Li PMCID: PMC1933147 Melina II: a web tool for comparisons among several predictive algorithms to find potential motifs from promoter regions Toshiyuki Okumura, Hiroki Makiguchi, Yuko Makita, Riu Yamashita, and Kenta Nakai PMCID: PMC1933176 The Gibbs Centroid Sampler William A. Thompson, Lee A. Newberg, Sean Conlan, Lee Ann McCue, and Charles E. Lawrence PMCID: PMC1933196 PAP: a comprehensive workbench for mammalian transcriptional regulatory sequence analysis Li-Wei Chang, Burr R. Fontaine, Gary D. Stormo, and Rakesh Nagarajan PMCID: PMC1933204 oPOSSUM: integrated tools for analysis of regulatory motif over-representation Shannan J. Ho Sui, Debra L. Fulton, David J. Arenillas, Andrew T. Kwon, and Wyeth W. Wasserman PMCID: PMC1933229 STAMP: a web tool for exploring DNA-binding motif similarities Shaun Mahony and Panayiotis V. Benos PMCID: PMC1933206 SCOPE: a web server for practical de novo motif discovery Jonathan M. Carlson, Arijit Chakravarty, Charles E. DeZiel, and Robert H. Gross PMCID: PMC1933170 LTR_FINDER: an efficient tool for the prediction of full-length LTR retrotransposons Zhao Xu and Hao Wang PMCID: PMC1933203 RTAnalyzer: a web application for finding new retrotransposons and detecting L1 retrotransposition signatures Jean-François Lucier, Jonathan Perreault, Jean-François Noël, Gilles Boire, and Jean-Pierre Perreault PMCID: PMC1933146 FluGenome: a web tool for genotyping influenza A virus Guoqing Lu, Thaine Rowley, Rebecca Garten, and Ruben O. Donis PMCID: PMC1933150 FLAN: a web server for influenza virus genome annotation Yiming Bao, Pavel Bolotov, Dmitry Dernovoy, Boris Kiryutin, and Tatiana Tatusova PMCID: PMC1933127 SplicePort—An interactive splice-site analysis tool Rezarta Islamaj Dogan, Lise Getoor, W. John Wilbur, and Stephen M. Mount PMCID: PMC1933122 BIPASS: BioInformatics Pipeline Alternative Splicing Services Zoé Lacroix, Christophe Legendre, Louiqa Raschid, and Ben Snyder PMCID: PMC1933140 ASTALAVISTA: dynamic and flexible analysis of alternative splicing events in custom gene datasets Sylvain Foissac and Michael Sammeth PMCID: PMC1933205 RADAR: a web server for RNA data analysis and research Mugdha Khaladkar, Vivian Bellofatto, Jason T. L. Wang, Bin Tian, and Bruce A. Shapiro PMCID: PMC1933136 RNAbor: a web server for RNA structural neighbors Eva Freyhult, Vincent Moulton, and Peter Clote PMCID: PMC1933207 INFO-RNA—a server for fast inverse RNA folding satisfying sequence constraints Anke Busch and Rolf Backofen PMCID: PMC1933236 RSRE: RNA structural robustness evaluator Wenjie Shu, Xiaochen Bo, Zhiqiang Zheng, and Shengqi Wang PMCID: PMC1933138 pknotsRG: RNA pseudoknot folding including near-optimal structures and sliding windows Jens Reeder, Peter Steffen, and Robert Giegerich PMCID: PMC1933184 taveRNA: a web suite for RNA algorithms and applications Cagri Aksay, Raheleh Salari, Emre Karakoc, Can Alkan, and S. Cenk Sahinalp PMCID: PMC1933159 RNA Movies 2: sequential animation of RNA secondary structures Alexander Kaiser, Jan Krüger, and Dirk J. Evers PMCID: PMC1933240 The RNAz web server: prediction of thermodynamically stable and evolutionarily conserved RNA structures Andreas R. Gruber, Richard Neuböck, Ivo L. Hofacker, and Stefan Washietl PMCID: PMC1933143 MiPred: classification of real and pseudo microRNA precursors using random forest prediction model with combined features Peng Jiang, Haonan Wu, Wenkai Wang, Wei Ma, Xiao Sun, and Zuhong Lu PMCID: PMC1933124 CPC: assess the protein-coding potential of transcripts using sequence features and support vector machine Lei Kong, Yong Zhang, Zhi-Qiang Ye, Xiao-Qiao Liu, Shu-Qi Zhao, Liping Wei, and Ge Gao PMCID: PMC1933232 TFAM 1.0: an online tRNA function classifier Helena Tåquist, Yuanyuan Cui, and David H. Ardell PMCID: PMC1933168 DOMAC: an accurate, hybrid protein domain prediction server Jianlin Cheng PMCID: PMC1933197 PI2PE: protein interface/interior prediction engine Harianto Tjong, Sanbo Qin, and Huan-Xiang Zhou PMCID: PMC1933225 M4T: a comparative protein structure modeling server Narcis Fernandez-Fuentes, Carlos J. Madrid-Aliste, Brajesh Kumar Rai, J. Eduardo Fajardo, and András Fiser PMCID: PMC1933164 Pcons.net: protein structure prediction meta server Björn Wallner, Per Larsson, and Arne Elofsson PMCID: PMC1933226 MolProbity: all-atom contacts and structure validation for proteins and nucleic acids Ian W. Davis, Andrew Leaver-Fay, Vincent B. Chen, Jeremy N. Block, Gary J. Kapral, Xueyi Wang, Laura W. Murray, W. Bryan Arendall, III, Jack Snoeyink, Jane S. Richardson, and David C. Richardson PMCID: PMC1933162 Structure SNP (StSNP): a web server for mapping and modeling nsSNPs on protein structures with linkage to metabolic pathways Alper Uzun, Chesley M. Leslin, Alexej Abyzov, and Valentin Ilyin PMCID: PMC1933130 DBAli tools: mining the protein structure space Marc A. Marti-Renom, Ursula Pieper, M. S. Madhusudhan, Andrea Rossi, Narayanan Eswar, Fred P. Davis, Fátima Al-Shahrour, Joaquín Dopazo, and Andrej Sali PMCID: PMC1933139 eF-seek: prediction of the functional sites of proteins by searching for similar electrostatic potential and molecular surface shape Kengo Kinoshita, Yoichi Murakami, and Haruki Nakamura PMCID: PMC1933152 NQ-Flipper: recognition and correction of erroneous asparagine and glutamine side-chain rotamers in protein structures Christian X. Weichenberger and Manfred J. Sippl PMCID: PMC1933125 ProSA-web: interactive web service for the recognition of errors in three-dimensional structures of proteins Markus Wiederstein and Manfred J. Sippl PMCID: PMC1933241 QSCOP-BLAST—fast retrieval of quantified structural information for protein sequences of unknown structure Stefan J. Suhrer, Markus Gruber, and Manfred J. Sippl PMCID: PMC1933160 3dLOGO: a web server for the identification, analysis and use of conserved protein substructures Allegra Via, Daniele Peluso, Pier Federico Gherardini, Emanuele de Rinaldis, Teresa Colombo, Gabriele Ausiello, and Manuela Helmer-Citterich PMCID: PMC1933223 pKNOT: the protein KNOT web server Yan-Long Lai, Shih-Chung Yen, Sung-Huan Yu, and Jenn-Kang Hwang PMCID: PMC1933195 Protein knot server: detection of knots in protein structures Grigory Kolesov, Peter Virnau, Mehran Kardar, and Leonid A. Mirny PMCID: PMC1933242 Advantages of combined transmembrane topology and signal peptide prediction—the Phobius web server Lukas Käll, Anders Krogh, and Erik L.L. Sonnhammer PMCID: PMC1933244 MyHits: improvements to an interactive resource for analyzing protein sequences Marco Pagni, Vassilios Ioannidis, Lorenzo Cerutti, Monique Zahn-Zabal, C. Victor Jongeneel, Jörg Hau, Olivier Martin, Dmitri Kuznetsov, and Laurent Falquet PMCID: PMC1933190 fastSCOP: a fast web server for recognizing protein structural domains and SCOP superfamilies Chi-Hua Tung and Jinn-Moon Yang PMCID: PMC1933144 ProtSweep, 2Dsweep and DomainSweep: protein analysis suite at DKFZ C. del Val, P. Ernst, M Falkenhahn, C. Fladerer, K. H. Glatting, S. Suhai, and A. Hotz-Wagenblatt PMCID: PMC1933246 SH3-Hunter: discovery of SH3 domain interaction sites in proteins Enrico Ferraro, Daniele Peluso, Allegra Via, Gabriele Ausiello, and Manuela Helmer-Citterich PMCID: PMC1933191 The SLiMDisc server: short, linear motif discovery in proteins Norman E. Davey, Richard J. Edwards, and Denis C. Shields PMCID: PMC1933137 PrDOS: prediction of disordered protein regions from amino acid sequence Takashi Ishida and Kengo Kinoshita PMCID: PMC1933209 iPDA: integrated protein disorder analyzer Chung-Tsai Su, Chien-Yu Chen, and Chen-Ming Hsu PMCID: PMC1933224 PIC: Protein Interactions Calculator K. G. Tina, R. Bhadra, and N. Srinivasan PMCID: PMC1933215 MinActionPath: maximum likelihood trajectory for large-scale structural transitions in a coarse-grained locally harmonic energy landscape Joel Franklin, Patrice Koehl, Sebastian Doniach, and Marc Delarue PMCID: PMC1933200 PMG: online generation of high-quality molecular pictures and storyboarded animations Ludovic Autin and Pierre Tufféry PMCID: PMC1933120 siteFiNDER|3D: a web-based tool for predicting the location of functional sites in proteins C. Axel Innis PMCID: PMC1933183 Sequence harmony: detecting functional specificity from alignments K. Anton Feenstra, Walter Pirovano, Klaas Krab, and Jaap Heringa PMCID: PMC1933219 FRalanyzer: a tool for functional analysis of fold-recognition sequence–structure alignments Harpreet Kaur Saini and Daniel Fischer PMCID: PMC1933221 PAR-3D: a server to predict protein active site residues Kshama Goyal, Debasisa Mohanty, and Shekhar C. Mande PMCID: PMC1933233 Selecton 2007: advanced models for detecting positive and purifying selection using a Bayesian inference approach Adi Stern, Adi Doron-Faigenboim, Elana Erez, Eric Martz, Eran Bacharach, and Tal Pupko PMCID: PMC1933148 A server and database for dipole moments of proteins Clifford E. Felder, Jaime Prilusky, Israel Silman, and Joel L. Sussman PMCID: PMC1933167 PDB2PQR: expanding and upgrading automated preparation of biomolecular structures for molecular simulations Todd J. Dolinsky, Paul Czodrowski, Hui Li, Jens E. Nielsen, Jan H. Jensen, Gerhard Klebe, and Nathan A. Baker PMCID: PMC1933214 Patch Finder Plus (PFplus): A web server for extracting and displaying positive electrostatic patches on protein surfaces Shula Shazman, Gershon Celniker, Omer Haber, Fabian Glaser, and Yael Mandel-Gutfreund PMCID: PMC1933175 The RCI server: rapid and accurate calculation of protein flexibility using chemical shifts Mark V. Berjanskii and David S. Wishart PMCID: PMC1933179 CytoSVM: an advanced server for identification of cytokine-receptor interactions Jin-Rui Xu, Jing-Xian Zhang, Bu-Cong Han, Liang Liang, and Zhi-Liang Ji PMCID: PMC1933174 ProMateus—an open research approach to protein-binding sites analysis Hani Neuvirth, Uri Heinemann, David Birnbaum, Naftali Tishby, and Gideon Schreiber PMCID: PMC1933218 MODPROPEP: a program for knowledge-based modeling of protein–peptide complexes Narendra Kumar and Debasisa Mohanty PMCID: PMC1933231 FastContact: a free energy scoring tool for protein–protein complex structures P. Christoph Champ and Carlos J. Camacho PMCID: PMC1933237 3D-partner: a web server to infer interacting partners and binding models Yung-Chiang Chen, Yu-Shu Lo, Wen-Chang Hsu, and Jinn-Moon Yang PMCID: PMC1933210 Frog: a FRee Online druG 3D conformation generator T. Bohme Leite, D. Gomes, M.A. Miteva, J. Chomilier, B.O. Villoutreix, and P. Tufféry PMCID: PMC1933180 firestar—prediction of functionally important residues using structural templates and alignment reliability Gonzalo López, Alfonso Valencia, and Michael L. Tress PMCID: PMC1933227 RNABindR: a server for analyzing and predicting RNA-binding sites in proteins Michael Terribilini, Jeffry D. Sander, Jae-Hyung Lee, Peter Zaback, Robert L. Jernigan, Vasant Honavar, and Drena Dobbs PMCID: PMC1933119 WoLF PSORT: protein localization predictor Paul Horton, Keun-Joon Park, Takeshi Obayashi, Naoya Fujita, Hajime Harada, C.J. Adams-Collier, and Kenta Nakai PMCID: PMC1933216 KinasePhos 2.0: a web server for identifying protein kinase-specific phosphorylation sites based on sequences and coupling patterns Yung-Hao Wong, Tzong-Yi Lee, Han-Kuen Liang, Chia-Mao Huang, Ting-Yuan Wang, Yi-Huan Yang, Chia-Huei Chu, Hsien-Da Huang, Ming-Tat Ko, and Jenn-Kang Hwang PMCID: PMC1933228 CanPredict: a computational tool for predicting cancer-associated missense mutations Joshua S. Kaminker, Yan Zhang, Colin Watanabe, and Zemin Zhang PMCID: PMC1933186 Zinc Finger Targeter (ZiFiT): an engineered zinc finger/target site design tool Jeffry D. Sander, Peter Zaback, J. Keith Joung, Daniel F. Voytas, and Drena Dobbs PMCID: PMC1933188 LIPID MAPS online tools for lipid research Eoin Fahy, Manish Sud, Dawn Cotter, and Shankar Subramaniam PMCID: PMC1933166 MetaPath Online: a web server implementation of the network expansion algorithm Thomas Handorf and Oliver Ebenhöh PMCID: PMC1933239 DEEP—A tool for differential expression effector prediction Jost Degenhardt, Martin Haubrock, Jürgen Dönitz, Edgar Wingender, and Torsten Crass PMCID: PMC1933247 VisANT 3.0: new modules for pathway visualization, editing, prediction and construction Zhenjun Hu, David M. Ng, Takuji Yamada, Chunnuan Chen, Shuichi Kawashima, Joe Mellor, Bolan Linghu, Minoru Kanehisa, Joshua M. Stuart, and Charles DeLisi PMCID: PMC1933155 INDELSCAN: a web server for comparative identification of species-specific and non-species-specific insertion/deletion events Feng-Chi Chen, Chueng-Jong Chen, and Trees-Juen Chuang PMCID: PMC1933116 RE-MuSiC: a tool for multiple sequence alignment with regular expression constraints Yun-Sheng Chung, Wei-Hsun Lee, Chuan Yi Tang, and Chin Lung Lu PMCID: PMC1933182 The M-Coffee web server: a meta-method for computing multiple sequence alignments by combining alternative alignment methods Sebastien Moretti, Fabrice Armougom, Iain M. Wallace, Desmond G. Higgins, Cornelius V. Jongeneel, and Cedric Notredame PMCID: PMC1933118 PROMALS web server for accurate multiple protein sequence alignments Jimin Pei, Bong-Hyun Kim, Ming Tang, and Nick V. Grishin PMCID: PMC1933189 COMPASS server for remote homology inference Ruslan I. Sadreyev, Ming Tang, Bong-Hyun Kim, and Nick V. Grishin PMCID: PMC1933213 DIAL: a web server for the pairwise alignment of two RNA three-dimensional structures using nucleotide, dihedral angle and base-pairing similarities F. Ferrè, Y. Ponty, W. A. Lorenz, and Peter Clote PMCID: PMC1933154 Multiple whole genome alignments and novel biomedical applications at the VISTA portal Michael Brudno, Alexander Poliakov, Simon Minovitsky, Igor Ratnere, and Inna Dubchak PMCID: PMC1933192 eProbalign: generation and manipulation of multiple sequence alignments using partition function posterior probabilities Satish Chikkagoudar, Usman Roshan, and Dennis Livesay PMCID: PMC1933135 BLASTO: a tool for searching orthologous groups Yi Zhou and Laura F. Landweber PMCID: PMC1933156 SePaCS—a web-based application for classification of seroreactivity profiles Andreas Keller, Nicole Comtesse, Nicole Ludwig, Eckart Meese, and Hans-Peter Lenhof PMCID: PMC1933220 BioBayesNet: a web server for feature extraction and Bayesian network modeling of biological sequence data Swetlana Nikolajewa, Rainer Pudimat, Michael Hiller, Matthias Platzer, and Rolf Backofen PMCID: PMC1933181 EVALLER: a web server for in silico assessment of potential protein allergenicity Alvaro Martinez Barrio, Daniel Soeria-Atmadja, Anders Nistér, Mats G. Gustafsson, Ulf Hammerling, and Erik Bongcam-Rudloff PMCID: PMC1933222 ProSight PTM 2.0: improved protein identification and characterization for top down mass spectrometry Leonid Zamdborg, Richard D. LeDuc, Kevin J. Glowacz, Yong-Bin Kim, Vinayak Viswanathan, Ian T. Spaulding, Bryan P. Early, Eric J. Bluhm, Shannee Babai, and Neil L. Kelleher PMCID: PMC1933126 The Multi-Q web server for multiplexed protein quantitation Chuan-Yih Yu, Yin-Hao Tsui, Yi-Hwa Yian, Ting-Yi Sung, and Wen-Lian Hsu PMCID: PMC1933177 DSHIFT: a web server for predicting DNA chemical shifts Sik Lok Lam PMCID: PMC1933157 CrystTwiV: a webserver for automated phase extension and refinement in X-ray crystallography Trias Thireou, Vassilis Atlamazoglou, Manolis Levakis, Elias Eliopoulos, Athanassios Hountas, George Tsoucaris, and Kostas Bethanis PMCID: PMC1933117 |
